Endogenous lentivirus in Malayan colugo (Galeopterus variegatus), a close relative of primates

Abstract

BackgroundA significant fraction of mammalian genomes is composed of endogenous retroviral (ERV) sequences that are formed by germline infiltration of various retroviruses. In contrast to other retroviral genera, lentiviruses only rarely form ERV copies. We performed a computational search aimed at identification of novel endogenous lentiviruses in vertebrate genomes.FindingsUsing the in silico strategy, we have screened 104 publicly available vertebrate genomes for the presence of endogenous lentivirus sequences. In addition to the previously described cases, the search revealed the presence of endogenous lentivirus in the genome of Malayan colugo (Galeopterus variegatus). At least three complete copies of this virus, denoted ELVgv, were detected in the colugo genome, and approximately one hundred solo LTR sequences. The assembled consensus sequence of ELVgv had typical lentivirus genome organization including three predicted accessory genes. Phylogenetic analysis placed this virus as a distinct subgroup within the lentivirus genus. The time of insertion into the dermopteran lineage was estimated to be more than thirteen million years ago.ConclusionsWe report the discovery of the first endogenous lentivirus in the mammalian order Dermoptera, which is a taxon close to the Primates. Lentiviruses have infiltrated the mammalian germline several times across millions of years. The colugo virus described here represents possibly the oldest documented endogenization event and its discovery can lead to new insights into lentivirus evolution. This is also the first report of an endogenous lentivirus in an Asian mammal, indicating a long-term presence of this retrovirus family in Asian continent.Electronic supplementary materialThe online version of this article (doi:10.1186/s12977-014-0084-x) contains supplementary material, which is available to authorized users.

Potential for virus endogenization in humans through testicular germ cell infection: the case of HIV

“…Such integration, still ongoing in mammals [4], has driven the acquisition of new functions in the host, including a protective role against exogenous infections [5,6]. Within the retrovirus family, several lentiviruses have been endogenized in mammals, including SIV in pro-lemurians [7–12]. A few non-retroviruses have also colonized the germline of their host but the mechanisms for their integration are unclear [1].…”

Deltaretroviruses have circulated since at least the Paleogene and infected a broad range of mammalian species

“…We obtained all available mammalian genomes as of February 2019. These data were screened for deltaretrovirus-derived ERVs using the basic local alignment search tool (BLAST) program suite, as described previously [12, 22]. Query sequences were derived from exogenous deltaretrovirus genomes and known deltaretrovirus-derived ERVs (MinERVa: KY250075).…”

“…We can only draw tentative conclusions here, because almost all published WGS are to some extent incomplete, but based on current information this consistently single-copy nature appears to be a unique feature of deltaretrovirus endogenization. By contrast, endogenous lentiviruses (which also only occur sporadically) typically occur as multicopy lineages in the species that harbour them [12–17]. One possibility is that efficient germline propagation of endogenous deltaretroviruses is prevented by efficient epigenetic silencing in germline cells [18, 19] or by efficient blocking of cell entry receptors by Env proteins encoded by endogenous deltaretroviruses.…”

Vpr and Its Cellular Interaction Partners: R We There Yet?

“…Some accessory open reading frames have also been described for the oldest integrations of lentiviruses. However, none of these open reading frames has been assigned to Vpr indicating that vpr is a more recently acquired accessory gene [2,3].…”